I don't how our Jeeps can all be so different. I'm running 33's on stock suspension and gearing and have never used 6th gear. Even at 75+ un the freeway 6th gear is useless unless I'm going downhill. Pulling a 1% grade in 6th is laughable. I would really like to re-gear.
I wouldn't be too concerned with the replacement engine. It sounds like the dealer is doing everything possible to make the situation right for you. If you ordered the Jeep exactly the way you wanted it, I'd let them put the new engine in and enjoy it.